Sunday, 25 August 2013

P2PU Open Research or-3: How Can We Research Openly?

Ooh, more new things I hadn't heard of!

Google Fusion Tables look very interesting, I'm sure I can shoehorn them into a piece of work in future (look out world, cue evil laugh...), but for now have a read of this description of how to use a visualisation tool called Gephi: http://linkedscience.org/tools/sparql-package-for-r/sparql-package-for-r-gephi-movie-star-graph-visualization-tutorial/

The image below (from Matt Biddulph on Flickr) shows what Gephi can do:
The true continents of the world (version 2)

My Britishness slips again as once more I say...awesome!

Thursday, 22 August 2013

P2PU Open Research or-2: Who's Working On It?

A few months ago I had a Eureka moment when I finally understood how valuable Twitter could be. I mostly use it for finding out local information, headline news, and information relating to open access (such an interesting life I lead).

There are 2 people whose tweets I particularly look forward to reading: Greg Jenner (@greg_jenner), the Horrible Histories historian, and Jon Tennant (@Protohedgehog) who is "PhD-ing with dinosaurs".

Jon Tennant is a great 'open' advocate; this is how science should be! On his blog he talks about the Palaeobiology Database:

The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It has expanded continuously since 2000 thanks to the efforts of 340 paleontologists from around the world.

He uploaded his 9 month PhD report to Figshare and, via Twitter, has massively increased my knowledge of, and interest in, open science.

Jon Tennant, I salute you!

P2PU Open Research or-1: What Makes it Open?

Open Research is the next logical step forward from Open Access and Open Data.


Open Access enables you to share your research findings with everyone.

Open Data lets you share the data you have collected with everyone.

Open Research allows you to share not only your complete methodology and software code that you are using to obtain your data, but also allows you to share your data as you are collecting it. Faster results, greater collaboration, reproducible experiments, further scientific advancement.

Want an example of how this works? Have a look at the Open Research Exchange.

Data and Merlin
I can haz data
And I can haz data too
(Photo from Melissa Wiese on Flickr)

Sunday, 18 August 2013

P2PU Open Data od-4: What Can I Do?

Now bear in mind that I'm British so I should be saying "this is rather good, chaps", but in fact it is awesome!

I've signed up to SciStarter so I can contribute to scientific research from the comfort of my own home. There are so many interesting projects listed, including Notes From Nature (transcribing labels of historical museum collections) that I've got bookmarked to contribute to when I have more time, and Treezilla (mapping every tree in Britain) but I was disappointed to find projects listed that had finished, and projects that involve further registration instead of the SciStarter login being sufficient.

I have just taken part in the VerbCorner Project, answering questions about the use of words. You can login or take part anonymously and it's great - challenging enough to be interesting, but not so hard that it is demoralising. So thank you SciStarter for linking me with the project and making me feel I have contributed!


P2PU Open Data od-3: What are the Current Issues?

Task 3 this week is:
Perform online field research about an Open Science Data Community, pinpointing a specific issue around Open Data that is being discussed right now. Note the following: What is the issue at hand? Who is talking about the issue? What organizations/institutions do they represent? Where can we go for more information about this issue?

A search on Twitter using the #opendata hashtag and a couple of idle Google searches (delayed slightly while I put the hood of my jumper up and couldn't resist doing a Sith lord impression - chilly and rainy in south England this evening) drew me into reading about issues relating to where data should be stored.

I have a vague awareness of the background to this at my place of work (not the Death Star, fear not); the University of Southampton was involved in a JISC project from 2009-2011 titled IDMB: Institutional data management blueprint that led on to another project, DataPool, both of which I was aware of but not knowledgable about.

From this the decision was made to use the existing institutional repository, ePrints Soton, to store datasets, as explained here. I know a bit about this because I helped test the ReCollect plug-in that deals with the data deposit workflow.

But how do people know where to find or deposit open data? Should it be in a subject repository or an institutional repository? The good news is that there are a lot of open data repositories, as listed on the Open Access Directory (OAD) wiki. The even better news is that there are a lot of people out there who know a lot more about it than me.


Death Star II

Thursday, 15 August 2013

P2PU Open Data od-2: How Open Is it?

For this task we were asked to assess the openness of one of 3 specified repositories. I chose the NASA Life Science Data Repositories (well, who would turn down the chance to look at stuff related to space? It's way up there with dinosaurs and cartoons from the 80s).

The 'about the archive' section states:

NASA's Life Sciences Data Archive (LSDA) is an active archive that provides information and data from 1961 (Mercury Project) through current flight and flight analog studies (International Space Station, Shuttle, bed rest studies, etc.) involving human, plant and animal subjects. 

Much of the information and data are publicly available on this site. Some data are potentially attributable to individual human subjects, and thus restricted by the Privacy Act, but can be requested for research.

Sounds good so far, so let's check...

Can you view the datasets at no cost? Must you sign up to view the data?
I checked several datasets; all were easy to view (as an Excel spreadsheet). I did not need to sign up.

Is there a tool on the website for you to view or manipulate the data?
I don't think so (although I'm not entirely sure what I'm looking for), but all the data I looked at is in Excel spreadsheets which are easy to manipulate.*

Can you download the datasets from the repository?
Yes, all the ones I checked could be downloaded.

Are the licenses for the datasets clearly marked and visible? What licenses are on the datasets?
I could not find any license information. I tried doing a full-text search for CC-BY then a search for "public domain" but both returned no results. I assume the datasets are freely available for re-use but it would be good practice if this was explicitly stated.

The LSDA site also has a photo gallery but again I could not find any license information, so here is a CC-BY-NC licensed photo from Flickr:


Space Shuttle Endeavour Over Earth (NASA, International Space Station Science, 02/09/10)
http://www.flickr.com/photos/nasamarshall/4358541558/


*by those who know what they are doing, not by me just in case anyone has plans to give me a load of spreadsheets!

Tuesday, 13 August 2013

P2PU Open Data od-1: What is Open Data?

New territory for me this week after the comfort zone of open access last week, and our first task is to define open data in our own words.

Open data is freely available to anyone (either under a CC-BY license or equivalent if required or in the public domain) so it can be reused and redistributed without restriction. The benefits are huge; opening up the availability of data sets provides more research and collaboration opportunities. Barriers are where to store/find the data, the quality of metadata, and the format the data is stored in...oh, and persuading people to make their data open!

I would rate my knowledge of open data 2 out of 5.

Wednesday, 7 August 2013

P2PU Open Science: oa-2, oa-3 and oa-4

OA-2 - How Open Is It?

For the oa-2 task we were asked to assess the openness of an electronic resource, such as a journal article. I selected mine by Googling "chocolate and journal article" and clicking on the first link to an article rather than a news resource that came up:

Linthwaite, S. and Fuller, Geraint N. (2013) Milk, chocolate and Nobel prizes. Practical Neurology 13:63  http://dx.doi.org/10.1136/practneurol-2012-000471

So, how open is it?

Reader rights: restricted to subscription only

Reuse rights: None: "BMJ Group offers the Copyright Clearance Centre's Rightslink licensing solution for ALL reuse permissions". So I could pay £337.66 to use the article on my website for 3 months.
Copyrights: held by the publisher: Copyright © 2013, British Medical Journal Publishing Group
Author posting rights: I looked this up on Sherpa Romeo and found that Practical Neurology allows the archiving of a pre-print on an author page or institutional repository. Post-prints can be archived with a 6 month embargo (Sherpa Romeo states 12 months for PubMed but Sherpa FACT states 6 months). The publisher version may not be archived anywhere by the author.
Automatic posting: I don't think this happens, although had the author used the journal's paid open access option it would be automatically posted in Europe PMC/Pubmed Central at the time of publication)
Metadata readability: I'm not sure how to find this out.


Looks like I don't get to find out or share any more about the strong correlation between a nation's chocolate consumption with the country's prowess in winning Nobel prizes per capita!


OA-3: Where's the OA?

I chose "spinach and health" as the area of research that interests me (felt I should counter-balance the chocolate example above).
I used the CORE (COnnecting REpositories) search tool to find my first article:
This one looked interesting (although more about health than spinach): Little, Max; Wicks, Paul; Vaughan, Timothy and Pentland, Alex (2013). Quantifying short-term dynamics of Parkinson's disease using self-reported symptom data from an internet social network. Journal of medical internet research, 15 (1).  It came from the Aston University eprints repository and had the license information (CC-BY) in the additional information field.

I wanted to try a different search tool to find my other 2 articles and selected Google Scholar. I searched for 'spinach and health open access' and chose:

Sakamaki, R. et al (2005) Nutritional knowledge, food habits and health attitude of Chinese university students –a cross sectional study. 4:4. This has a CC-BY license.

van Grinsven, H.J.M. et al (2006) Does the evidence about health risks associated with nitrate
ingestion warrant an increase of the nitrate standard for drinking water? Environmental Health: A Global Access Science Source 2006, 5:26. This also has a CC-BY license.


Although I like the idea of the CORE search, Google Scholar provided more relevant and easier to refine results.

OA-4: What Can I Do?

This is a slight deviation from the specified upload (of my video describing OA-3, above) to You Tube or Slideshare. Unfortunately Dropbox, which is normally brilliant for moving content (such as a newly created video), from a tablet device to a computer is stubbornly showing an 'out of space' error.

So I have uploaded the video to Flickr instead and set the attribution to CC-BY. It should display nicely below on a PC but is a vast empty space below on an iPad so the link is   http://www.flickr.com/photos/nicki_clarkson/9459259247/
Here it is:

Tuesday, 6 August 2013

P2PU Open Science: Introduction & oa-1: What is Open Access?

The end of the New Librarianship MOOC (which I am delighted to say I get an emailed certificate of completion for as I passed all the tests... admittedly by retaking some of them multiple times but shhhh) coincides nicely with the beginning of my next online quest.

I am taking the P2PU course on Open Science:

This course is a collaborative learning environment meant to introduce the idea of Open Science to young scientists, academics, and makers of all kinds. Open Science is a tricky thing to define, but we've designed this course to share what we know about it; working as a community to make this open resource better. Think of it as a layer on top of the way science is commonly done now. Just better.

Instead of a discussion board our contribution takes the form of writing blog posts as a response to set topics, then sharing them with the other course participants. Here goes...

OA-1: What is Open Access?


Open Access refers to materials, commonly (but not exclusively) journal articles, that are free to all readers at the point of use. This relatively new movement is a change from the old model where research was funded (often by the government via the research councils in the UK) then the findings were published in a journal that was then only available to those individuals or institutions that had a subscription to that journal.

In 2012 the Finch report was published, as discussed in this article from the Guardian. This led to a new policy from RCUK (Research Councils UK) stating that as of April 1st 2013 the findings of all RCUK funded research must be made open access:

"Free and open access to the outputs of publicly-funded research offers significant social and economic benefits as well as aiding the development of new research. The Government, in line with its overarching commitment to transparency and open data, is committed to ensuring that published research findings should be freely accessible. As bodies charged with investing public money in research, the Research Councils take very seriously their responsibilities in making the outputs from this research publicly available – not just to other researchers, but also to potential users in business, charitable and public sectors, and to the general tax-paying public."

There are 2 routes to making articles open access:
Gold open access means that the publisher version of an article is made immediately available with no embargo period in a journal. This can either be in an open access (OA) only journal, or a hybrid journal that contains a mix of subscription and OA articles. Gold OA can require the payment of a fee, an Article Processing Charge (APC), to the journal publisher.
Green open access is where an author publishes in a journal and then deposits a version of the article into a subject or institutional repository. Generally publishers stipulate this has to be a post-print, so it has undergone peer review but does not have the publisher markings or layout. Some publishers impose an embargo period so the article cannot be made open access via the green route immediately.

Both gold and green OA have passionate advocates. If you are interested in finding out more, both views are aired in this Times Higher Education article from 2012.

You may hear the terms 'gratis' and 'libre' used to describe OA. These are additional to the green/gold (repository/journal) distinction: gratis OA refers to the removal of price barriers, whereas libre OA refers to the removal of both price and permissions barriers to allow the easy access and reuse of research.

You will also come across talk of Creative Commons licenses; they feature in the RCUK OA policy. This is from Section 3.7: Licences...

"(i) Where Research Council funds are used to pay the APC for an Open Access paper, we require that the publisher makes the paper freely available under a Creative Commons Attribution (CC BY) licence. This is the standard licence used by open access journals, and supports the maximum dissemination and re-use of published papers, whilst protecting the moral rights of authors. It allows others to distribute,remix, manipulate, and build upon a paper, including commercially, as long as they credit the authors for the original paper and do not infringe any copyrights to third-party material included in the paper. The use of CC BY where an APC is paid is also the policy of the Wellcome Trust.
(ii) The CC BY licence opens up possibilities for new areas of research by the re-use of papers, and the content of papers through text and data mining, and for new ways of disseminating research by being able to re-present papers in innovative and potentially value-adding ways. Crucially, the CC BY licence removes any doubt or ambiguity as to what may be done with papers, and allows re-use without having to go back to the publisher to check conditions or ask for specific permissions."

Open Access logo PLoS transparent

Monday, 5 August 2013

New Librarianship MOOC: Reflections

The course centred around the various parts making up the following mission statement:

The mission of librarians is to improve society through facilitating knowledge creation in their communities.

Hmm. I'm not sure that librarians need a mission statement. If anything it should be the library that has the mission statement, then the mission belongs to all members of staff and is available to the community, rather than being a grandiose (maybe even slightly pretentious) statement forced onto the community by the librarian.

The mission statement is a little too buzzwordy for my liking; it took a 4 week MOOC to untangle and explain it all. I like most of what it is saying (although the 'improve society' bit makes me cringe) but not the way it is said.

My other issue with the mission statement is that it is so generic. It applies not only to librarians but also to teachers and parents. Maybe each individual librarian should be asked to design their own mission statement. Or maybe it doesn't need to be articulated at all but is implicit within all librarians who care about doing a good job.

I found the course hard-going at times; I need a better understanding of the philosophy and theories underlying the course (such as conversation theory) to be able to join all the discussion board chats as an equal. I did not make any ground-breaking contributions. I found it a struggle to fit in watching all of the video lectures - podcasts I could have listened to while out running (admittedly only if they were very short), or transcripts I could have read on a lunch break, or with my children constructing Lego armies in the background. I wanted to watch each video in its entirity to make sure I didn't miss anything but sometimes I got to the end with a feeling of frustration that the material could have been covered more concisely.

However, there were times in the videos when I was nodding in agreement, or frowning in thought, or being delighted at hearing the theory demonstrated in a real life example. The enthusiasm, knowledge, articulateness (how's that for an oxymoron?) and level of conversation on the discussion boards was inspiring and it is great that the course participants respect other views even if they do not agree with them. I did not expect such a high degree of contribution to the discussion board topics from Prof Lankes, not only asking questions to initiate threads but joining in debates and asking further questions.

As a library assistant I am disheartened to realise (from reading discussion board comments) how vast some people perceive the skills gap between qualified and non-qualified library staff to be. Maybe this is more the case in public than academic libraries? Or maybe I have ideas above my station.

Am I glad I took this MOOC? Yes, but I'm also glad it has finished which is not such a stunning endorsement. Do I believe in New Librarianship? Yes, in that we should constantly innovate and engage with our communities.

As a Quester (yep, definitely works!) I am continuing my MOOC journey. I have signed up for a course on metadata (Coursera) and one on dinosaur paleobiology (dinosaurs! How could you not?) (Coursera again) and an open science online course (P2PU). Bring it on!


New Librarianship MOOC Week 4: Communities

Week 4 focused on communities and was divided into 4 modules:

Module 1 highlighted the idea that libraries should share rather than lend. Whereas lending is a one way street (allowing people to borrow from a common resource) sharing embraces active contributions from the community (in terms of time, expertise and physical 'stuff', such as sharing their own book collections) - combining resources together to make a richer commons. This came back to examples of libraries as makerspaces (there is a 3 part article on makerspaces from Library Journal here if you want to find out more  - I love it!).

How does this apply to academic libraries? Other than open access via institutional repositories, and future enhancements of the repositories so they are more social and connected I was stymied. So I asked the question on the discussion board and got some great answers:





I also came across this post on Making Things in Academic Libraries on the Association of College & Research Libraries (ACRL) blog. As often with online articles, the comments are as interesting as the post itself.


The second module, ominously titled 'kill the user' was about how best to trap unsuspecting users in the stacks...or it may have been about changing from the term 'user' (which along with 'patron' and 'customer' is very 'us versus them', seeing users as consumers) and the quest for a better term, such as 'member', 'participant' or (cringe) 'prosumer', which is a blend of professional/producer and consumer. I'm not encouraging the adoption of that last one as it sound very management buzzwordy, which will surely broaden the divide between library staff and 'users' when we seek to do the opposite.

I like talk of the 'community' to describe everyone engaging with the library but it is harder to find the perfect term to describe an individual using the library; maybe we could have an international contest to create a new word? How about 'libcomber' (library + community + member)? No? Or we could go with Quester - I would be happy with being a quester.

There were some interesting posts on the discussion board about how users of academic libraries are viewed, some copied below, although everybody agreed that anyone coming into the library would be treated with the same high level of customer service and respect:






The third module covered the deficit model of communities, which I felt applied more to public libraries than academic communities. Librarians should use advocacy (seeing opportunities and giving people skills to reach their aspirations ans enable participation) rather than remediation (trying to fix problems and inadvertently reminding communities of their failings). R. David Lankes explains this far better than I have so I will embed the video below. The module also introduced me to the concept of 'satisficing', a term I had not come across before.

Module 4 provided some criticisms of the New Librarianship approach which was refreshing to see. Although Prof Lankes offers up his theory of new librarianship I think the purpose of this MOOC was to allow us, the Questers (see, it works!) to examine our own thoughts and engage in conversations, to come up with our own theories and models and constantly re-evaluate them rather than to convince us all that he is right.